A clock and data recovery apparatus and the method thereof are applied for burst mode clock and data recovery (CDR) in a passive optical network (PON). A phase-locked loop induces a first control signal and a first clock. A clock and data recovery circuit receives an incoming data having a first frequency and induces a second clock having one of second and third frequencies to sample the incoming data according to the second clock to obtain a recovered data, wherein the first frequency is between the second and third frequencies. Moreover, a controller induces a second control signal according to the incoming data (or the recovered data), the first clock, and the second clock to adjust the frequency of the second clock.